In changing coastal environments, different driving forces can lead to freshwater salinization, which may cause vegetation mortality for low-saline tolerance plants and saltmarsh migration into uplands. Coastal flooding from storm surges and extreme high tides are fast forcing mechanisms that causes immediate responses in soil salinity. On the other hand, sea-level rise, which is relatively slow forcing, can lead to movement of saltwater inland and increase the salinity of the fresh groundwater system. Along the Delmarva Peninsula, USA, vegetation mortality and saltmarsh migration have been observed and monitored at six sites. In this work, a 3D HydroGeoSphere model is applied to a marsh-to-forest transition zone along the Atlantic Coastline in Virginia to study the effects of different forcings on salinity variations. Land surface depressions caused by uprooting of dead trees can change the soil properties and morphology. Preferential flow paths for saline floodwater infiltrating the subsurface can be caused by increased permeability of near-surface sediments. The resulting pits can also hold saline floodwater, potentially increasing the amount of salt infiltration. The current work investigates the influence of heterogeneity in permeability and land surface elevation caused by tree mortality and saltmarsh migration on saltwater intrusion to groundwater under both extreme events for storm surge sea-level rise. The work elucidates the integration of 3D groundwater-surface water interaction model and field measurement as well as the impact of permeability and morphology heterogeneity on saltwater intrusion and saltmarsh migration in changing coastal environments.